you can put it on our ftp site:

https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e=
but at that point you might as well tar and gzip the entire subject dir and upload it

On Wed, 31 May 2017, Jasmin Alves wrote:

Hi Bruce,
Thanks for the reply, below is a couple of sentences from the recon-all.log 

reading initial pial vertex positions from white.preaparc...

mean border=65.6, 300 (300) missing vertices, mean dist 2.2 [2.0 (%0.1)->3.2
(%99.9))]

%21 local maxima, %44 large gradients and %29 min vals, 639 gradients
ignored

perforing initial smooth deformation to move away from white surface

tol=1.0e-04, sigma=2.0, host=hpc17, nav=16, nbrs=2, l_surf_repulse=1.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000

mom=0.00, dt=0.05.


I also attached a screenshot of the log. 


Is there a place I should upload the files?


Thanks,

Jasmin 


On Wed, May 31, 2017 at 12:28 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Jasmin

      typically that means there is a big topological defect, which
      definitely can be caused by motion. What is the last couple of
      lines of the recon-all.log file of one of the subjects? Can you
      upload an image we can look at?

      cheers
      Bruce


      On Wed, 31 May 2017, Jasmin Alves wrote:

            Hello,
            I have used FS6.0 to do recon-all on about 57
            brains, but for some reason,
            recon-all is not working on some brains, recon-all
            is not able to get past
            "Automatic topology fixer", after the command has
            been running for 24 hours.

             Is it possible there is too much motion in the
            image? Or does FS6.0
            possibly take longer to complete for some brains?

            Thanks,
            Jasmin 

            --
            Jasmin Alves
            Doctoral Candidate 
            Medical Biology Graduate Program 
            University of Southern California
            jalves@usc.edu 



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--
Jasmin Alves
Doctoral Candidate 
Medical Biology Graduate Program 
University of Southern California
jalves@usc.edu 

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